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Summary

SOAP2.18 (short oligonucleotide analysis package) is a versatile and fast aligner for short reads. It uses the 2-way burrows-wheeler transform to reduce the amount of memory needed while mapping. It handles only base space data.

in.csfasta&nbsp;: reads file in color space
in.m.fasta&nbsp;: reads file in mock base space
\-d&nbsp;: drop the first colorspace base during conversion. This will ignore the first color space base which is part of the primer.
\-r&nbsp;: For each read, include the reverse of the mock base space sequence.

Troubleshooting

If you have lots of warning message as 'length y < 0, countinue as 13', it means that your read length is too short, so SOAP cannot handle them properly. Currently, SOAP supports only reads longer than 30 bp.( NewsGroup article; it described 2.18 version, but 2.20 shows the same result.)